Docking@Grid-A Web Portal for Massively Parallel Flexible Docking, using the ChemAxon Toolkit

presentation · 12 years ago
by Dragos Horvath (Université de Strasbourg, Centre National pour la Recherche Scientifique (CNRS))
Calculator Plugins (logP logD pKa etc...)

Within the framework of an ongoing, ANR (Agence Nationale de le Recherche) – funded project aimed at developing innovative flexible docking algorithms based on massively distributed GRID calculations, the web portail for the submission and analysis of docking runs by future Academic users is heavily relying on the ChemAxon toolkit, notably for the pre-docking treatment of the submitted potential ligands: 1.Standardized representation, including counterion detection/deletion (Standardizer) 2.Enumeration of microspecies and potential tautomeric forms according to a user-defined policy (dock major microspecies/tautomers, dock several microspecies/tautomers or dock compounds in protonation states as presented in the input file) 3.Fractional charge calculations for each microspecies/tautomer 4.Empirical force field typing for each microspecies/tautomer, using Pmapper with custom-made XML setup files 5.Generation of initial 3D structures as starting points for distributed conformational sampling and/or use of the ChemAxon conformer generator to provide a set of possible geometries for the unbound ligands 6.Storing of already built multiconformational sets of compounds, using JChem 7.2D/3D visualisation of individual ligands using mview and display of docking poses in mspace. The presentation will, after a brief discussion of the planned docking strategies and algorithms, make the point on the current progress on the seven above-mentioned aspects, highlighting the strengths and the wish list of improvements of involved ChemAxon tools.